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Lai WY, Chuang TP, Borenäs M, Lind DE, Hallberg B, Palmer RH. Anaplastic Lymphoma Kinase signaling stabilizes SLC3A2 expression via MARCH11 to promote neuroblastoma cell growth. Cell Death Differ 2024; 31:910-923. [PMID: 38858548 PMCID: PMC11239919 DOI: 10.1038/s41418-024-01319-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 05/23/2024] [Accepted: 05/28/2024] [Indexed: 06/12/2024] Open
Abstract
Solute Carrier Family 3, Member 2 (SLC3A2 or 4F2hc) is a multifunctional glycoprotein that mediates integrin-dependent signaling, acts as a trafficking chaperone for amino acid transporters, and is involved in polyamine transportation. We identified SLC3A2 as a potential Anaplastic Lymphoma Kinase (ALK) interacting partner in a BioID-proximity labeling screen in neuroblastoma (NB) cells. In this work we show that endogenous SLC3A2 and ALK interact in NB cells and that this SLC3A2:ALK interaction was abrogated upon treatment with the ALK inhibitor lorlatinib. We show here that loss of ALK activity leads to decreased SLC3A2 expression and reduced SLC3A2 protein stability in a panel of NB cell lines, while stimulation of ALK with ALKAL2 ligand resulted in increased SLC3A2 protein levels. We further identified MARCH11, an E3 ligase, as a regulator of SLC3A2 ubiquitination downstream of ALK. Further, knockdown of SLC3A2 resulted in inhibition of NB cell growth. To investigate the therapeutic potential of SLC3A2 targeting, we performed monotreatment of NB cells with AMXT-1501 (a polyamine transport inhibitor), which showed only moderate effects in NB cells. In contrast, a combination lorlatinib/AMXT-1501 treatment resulted in synergistic inhibition of cell growth in ALK-driven NB cell lines. Taken together, our results identify a novel role for the ALK receptor tyrosine kinase (RTK), working in concert with the MARCH11 E3 ligase, in regulating SLC3A2 protein stability and function in NB cells. The synergistic effect of combined ALK and polyamine transport inhibition shows that ALK/MARCH11/SLC3A2 regulation of amino acid transport is important for oncogenic growth and survival in NB cells.
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Affiliation(s)
- Wei-Yun Lai
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-40530, Gothenburg, Sweden
| | - Tzu-Po Chuang
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-40530, Gothenburg, Sweden
| | - Marcus Borenäs
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-40530, Gothenburg, Sweden
| | - Dan E Lind
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-40530, Gothenburg, Sweden
| | - Bengt Hallberg
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-40530, Gothenburg, Sweden.
| | - Ruth H Palmer
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-40530, Gothenburg, Sweden.
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Moaveni AK, Amiri M, Shademan B, Farhadi A, Behroozi J, Nourazarian A. Advances and challenges in gene therapy strategies for pediatric cancer: a comprehensive update. Front Mol Biosci 2024; 11:1382190. [PMID: 38836106 PMCID: PMC11149429 DOI: 10.3389/fmolb.2024.1382190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 03/27/2024] [Indexed: 06/06/2024] Open
Abstract
Pediatric cancers represent a tragic but also promising area for gene therapy. Although conventional treatments have improved survival rates, there is still a need for targeted and less toxic interventions. This article critically analyzes recent advances in gene therapy for pediatric malignancies and discusses the challenges that remain. We explore the innovative vectors and delivery systems that have emerged, such as adeno-associated viruses and non-viral platforms, which show promise in addressing the unique pathophysiology of pediatric tumors. Specifically, we examine the field of chimeric antigen receptor (CAR) T-cell therapies and their adaptation for solid tumors, which historically have been more challenging to treat than hematologic malignancies. We also discuss the genetic and epigenetic complexities inherent to pediatric cancers, such as tumor heterogeneity and the dynamic tumor microenvironment, which pose significant hurdles for gene therapy. Ethical considerations specific to pediatric populations, including consent and long-term follow-up, are also analyzed. Additionally, we scrutinize the translation of research from preclinical models that often fail to mimic pediatric cancer biology to the regulatory landscapes that can either support or hinder innovation. In summary, this article provides an up-to-date overview of gene therapy in pediatric oncology, highlighting both the rapid scientific progress and the substantial obstacles that need to be addressed. Through this lens, we propose a roadmap for future research that prioritizes the safety, efficacy, and complex ethical considerations involved in treating pediatric patients. Our ultimate goal is to move from incremental advancements to transformative therapies.
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Affiliation(s)
- Amir Kian Moaveni
- Pediatric Urology and Regenerative Medicine Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Amiri
- Pediatric Urology and Regenerative Medicine Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Behrouz Shademan
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Arezoo Farhadi
- Department of Genetics and Molecular Medicine, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Javad Behroozi
- Department of Cell and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Alireza Nourazarian
- Department of Basic Medical Sciences, Khoy University of Medical Sciences, Khoy, Iran
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Wang H, Yu C, Ding H, Zhang L, Chen X, He L. Computed Tomography-Based Radiomics Signature for Predicting Segmental Chromosomal Aberrations at 1p36 and 11q23 in Pediatric Neuroblastoma. J Comput Assist Tomogr 2024; 48:472-479. [PMID: 38013242 DOI: 10.1097/rct.0000000000001564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
OBJECTIVE This study aimed to develop and assess the precision of a radiomics signature based on computed tomography imaging for predicting segmental chromosomal aberrations (SCAs) status at 1p36 and 11q23 in neuroblastoma. METHODS Eighty-seven pediatric patients diagnosed with neuroblastoma and with confirmed genetic testing for SCAs status at 1p36 and 11q23 were enrolled and randomly stratified into a training set and a test set. Radiomics features were extracted from 3-phase computed tomography images and analyzed using various statistical methods. An optimal set of radiomics features was selected using a least absolute shrinkage and selection operator regression model to calculate the radiomics score for each patient. The radiomics signature was validated using receiver operating characteristic curves to obtain the area under the curve and 95% confidence interval (CI). RESULTS Eight radiomics features were carefully selected and used to compute the radiomics score, which demonstrated a statistically significant distinction between the SCAs and non-SCAs groups in both sets. The radiomics signature achieved an area under the curve of 0.869 (95% CI, 0.788-0.943) and 0.883 (95% CI, 0.753-0.978) in the training and test sets, respectively. The accuracy of the radiomics signature was 0.817 and 0.778 in the training and test sets, respectively. The Hosmer-Lemeshow test confirmed that the radiomics signature was well calibrated. CONCLUSIONS Computed tomography-based radiomics signature has the potential to predict SCAs at 1p36 and 11q23 in neuroblastoma.
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Affiliation(s)
- Haoru Wang
- From the Department of Radiology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing, China
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Bhatia S, Khanna KK, Duijf PHG. Targeting chromosomal instability and aneuploidy in cancer. Trends Pharmacol Sci 2024; 45:210-224. [PMID: 38355324 DOI: 10.1016/j.tips.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 02/16/2024]
Abstract
Cancer development and therapy resistance are driven by chromosomal instability (CIN), which causes chromosome gains and losses (i.e., aneuploidy) and structural chromosomal alterations. Technical limitations and knowledge gaps have delayed therapeutic targeting of CIN and aneuploidy in cancers. However, our toolbox for creating and studying aneuploidy in cell models has greatly expanded recently. Moreover, accumulating evidence suggests that seven conventional antimitotic chemotherapeutic drugs achieve clinical response by inducing CIN instead of mitotic arrest, although additional anticancer activities may also contribute in vivo. In this review, we discuss these recent developments. We also highlight new discoveries, which together show that 25 chromosome arm aneuploidies (CAAs) may be targetable by 36 drugs across 14 types of cancer. Collectively, these advances offer many new opportunities to improve cancer treatment.
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Affiliation(s)
- Sugandha Bhatia
- Queensland University of Technology (QUT), School of Biomedical Sciences, Centre for Genomics and Personalised Health and Centre for Biomedical Technologies at the Translational Research Institute, Woolloongabba, QLD 4102, Australia.
| | - Kum Kum Khanna
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD 4006, Australia; Mater Research Institute, The University of Queensland, Translational Research Institute, Woolloongabba, QLD 4102, Australia
| | - Pascal H G Duijf
- Queensland University of Technology (QUT), School of Biomedical Sciences, Centre for Genomics and Personalised Health and Centre for Biomedical Technologies at the Translational Research Institute, Woolloongabba, QLD 4102, Australia; Centre for Cancer Biology, Clinical and Health Sciences, University of South Australia and SA Pathology, Adelaide, SA 5001, Australia; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway; Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.
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5
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Borenäs M, Umapathy G, Lind DE, Lai WY, Guan J, Johansson J, Jennische E, Schmidt A, Kurhe Y, Gabre JL, Aniszewska A, Strömberg A, Bemark M, Hall MN, den Eynden JV, Hallberg B, Palmer RH. ALK signaling primes the DNA damage response sensitizing ALK-driven neuroblastoma to therapeutic ATR inhibition. Proc Natl Acad Sci U S A 2024; 121:e2315242121. [PMID: 38154064 PMCID: PMC10769851 DOI: 10.1073/pnas.2315242121] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 11/28/2023] [Indexed: 12/30/2023] Open
Abstract
High-risk neuroblastoma (NB) is a significant clinical challenge. MYCN and Anaplastic Lymphoma Kinase (ALK), which are often involved in high-risk NB, lead to increased replication stress in cancer cells, suggesting therapeutic strategies. We previously identified an ATR (ataxia telangiectasia and Rad3-related)/ALK inhibitor (ATRi/ALKi) combination as such a strategy in two independent genetically modified mouse NB models. Here, we identify an underlying molecular mechanism, in which ALK signaling leads to phosphorylation of ATR and CHK1, supporting an effective DNA damage response. The importance of ALK inhibition is supported by mouse data, in which ATRi monotreatment resulted in a robust initial response, but subsequent relapse, in contrast to a 14-d ALKi/ATRi combination treatment that resulted in a robust and sustained response. Finally, we show that the remarkable response to the 14-d combined ATR/ALK inhibition protocol reflects a robust differentiation response, reprogramming tumor cells to a neuronal/Schwann cell lineage identity. Our results identify an ability of ATR inhibition to promote NB differentiation and underscore the importance of further exploring combined ALK/ATR inhibition in NB, particularly in high-risk patient groups with oncogene-induced replication stress.
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Affiliation(s)
- Marcus Borenäs
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, GothenburgSE-405 30, Sweden
| | - Ganesh Umapathy
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, GothenburgSE-405 30, Sweden
| | - Dan E. Lind
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, GothenburgSE-405 30, Sweden
| | - Wei-Yun Lai
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, GothenburgSE-405 30, Sweden
| | - Jikui Guan
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, GothenburgSE-405 30, Sweden
| | - Joel Johansson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, GothenburgSE-405 30, Sweden
| | - Eva Jennische
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, GothenburgSE-405 30, Sweden
| | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum, Basel University, Basel4056, Switzerland
| | - Yeshwant Kurhe
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, GothenburgSE-405 30, Sweden
| | - Jonatan L. Gabre
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, GothenburgSE-405 30, Sweden
- Department of Human Structure and Repair, Anatomy and Embryology Unit, Ghent University, Ghent9000, Belgium
| | - Agata Aniszewska
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, GothenburgSE-405 30, Sweden
| | - Anneli Strömberg
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, GothenburgSE-405 30, Sweden
| | - Mats Bemark
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, GothenburgSE-405 30, Sweden
- Department of Clinical Immunology and Transfusion Medicine, Sahlgrenska University Hospital, Gothenburg SE-405 30, Sweden
| | | | - Jimmy Van den Eynden
- Department of Human Structure and Repair, Anatomy and Embryology Unit, Ghent University, Ghent9000, Belgium
| | - Bengt Hallberg
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, GothenburgSE-405 30, Sweden
| | - Ruth H. Palmer
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, GothenburgSE-405 30, Sweden
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Katic L, Priscan A. Multifaceted Roles of ALK Family Receptors and Augmentor Ligands in Health and Disease: A Comprehensive Review. Biomolecules 2023; 13:1490. [PMID: 37892172 PMCID: PMC10605310 DOI: 10.3390/biom13101490] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/02/2023] [Accepted: 10/06/2023] [Indexed: 10/29/2023] Open
Abstract
This review commemorates the 10-year anniversary of the discovery of physiological ligands Augα (Augmentor α; ALKAL2; Fam150b) and Augβ (Augmentor β; ALKAL1; Fam150a) for anaplastic lymphoma kinase (ALK) and leukocyte tyrosine kinase (LTK), previously considered orphan receptors. This manuscript provides an in-depth review of the biophysical and cellular properties of ALK family receptors and their roles in cancer, metabolism, pain, ophthalmology, pigmentation, central nervous system (CNS) function, and reproduction. ALK and LTK receptors are implicated in the development of numerous cancers, and targeted inhibition of their signaling pathways can offer therapeutic benefits. Additionally, ALK family receptors are involved in regulating body weight and metabolism, modulating pain signaling, and contributing to eye development and pigmentation. In the CNS, these receptors play a role in synapse modulation, neurogenesis, and various psychiatric pathologies. Lastly, ALK expression is linked to reproductive functions, with potential implications for patients undergoing ALK inhibitor therapy. Further research is needed to better understand the complex interactions of ALK family receptors and Aug ligands and to repurpose targeted therapy for a wide range of human diseases.
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Affiliation(s)
- Luka Katic
- Department of Medicine, Icahn School of Medicine at Mount Sinai Morningside/West, 1000 Tenth Avenue, New York, NY 10019, USA
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Anamarija Priscan
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA;
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Bahmad HF, Trinh S, Qian L, Terp K, Alloush F, Elajami MK, Kilinc E, Poppiti R. Colonic Ganglioneuroma: A Combined Single-Institution Experience and Review of the Literature of Forty-Three Patients. Diseases 2023; 11:diseases11020069. [PMID: 37218882 DOI: 10.3390/diseases11020069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/29/2023] [Accepted: 05/04/2023] [Indexed: 05/24/2023] Open
Abstract
Ganglioneuromas (GNs) are rare, benign tumors composed of ganglion cells, nerve fibers, and glial cells. Three types of colonic GN lesions exist: polypoid GNs, ganglioneuromatous polyposis, and diffuse ganglioneuromatosis. Less than 100 cases of GN are documented in the literature. A 10-year retrospective search of the pathology database at our institution identified eight cases of colonic GNs. All cases were incidental. Seven of the eight cases presented with colonoscopy findings of small sessile polyps (ranging between 0.1 and 0.7 cm) treated with polypectomy, whereas one case showed a 4 cm partially circumferential and partially obstructing mass in the ascending colon, treated with right hemicolectomy. Almost two-thirds of the cases (5/8) demonstrated associated diverticulosis. All cases were positive for S100 protein and Synaptophysin via immunohistochemistry (IHC). No syndromic association was identified in any of the cases. We also conducted a comprehensive review using PubMed to identify cases of colonic GN reported in the literature. In total, 173 studies were retrieved, among which 36 articles met our inclusion criteria (35 patients and 3 cases on animals). We conclude that while most GNs are incidental and solitary small sessile lesions, many can be diffuse and associated with syndromes. In these cases, the tumor can result in bowel obstruction simulating adenocarcinoma.
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Affiliation(s)
- Hisham F Bahmad
- Department of Pathology and Laboratory Medicine, Mount Sinai Medical Center, Miami Beach, FL 33140, USA
| | - Sally Trinh
- Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Linda Qian
- Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Kristy Terp
- Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Ferial Alloush
- Department of Pathology and Laboratory Medicine, Mount Sinai Medical Center, Miami Beach, FL 33140, USA
| | - Mohamad K Elajami
- Department of Internal Medicine, Mount Sinai Medical Center, Miami Beach, FL 33140, USA
| | - Ekim Kilinc
- Department of Pathology and Laboratory Medicine, Mount Sinai Medical Center, Miami Beach, FL 33140, USA
| | - Robert Poppiti
- Department of Pathology and Laboratory Medicine, Mount Sinai Medical Center, Miami Beach, FL 33140, USA
- Department of Pathology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
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Yue Z, Gao C, Xing T, Zhao W, Duan C, Wang X, Jin M, Su Y. Combined analysis of PHOX2B at two time points and its value for further risk stratification in high-risk neuroblastoma. Pediatr Blood Cancer 2023; 70:e30261. [PMID: 36815592 DOI: 10.1002/pbc.30261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 01/18/2023] [Accepted: 01/30/2023] [Indexed: 02/24/2023]
Abstract
BACKGROUND Risk stratification of high-risk neuroblastoma (NB) is crucial for exploring treatments. This study aimed to explore the value of minimal residual disease (MRD) based on PHOX2B levels for further risk stratification in high-risk NB. METHODS The expression of PHOX2B was monitored at two time points (after two and six cycles of induction chemotherapy, TP1 and TP2, respectively) by real-time polymerase chain reaction (RT-PCR). The clinical characteristics between groups and survival rates were analyzed. RESULTS The study included 151 high-risk patients. Positive expression of PHOX2B at diagnosis was seen in 129 cases. PHOX2B was mainly expressed in patients with high lactate dehydrogenase (LDH) and neuron-specific enolase (NSE) levels (p < .001), bone marrow metastasis (p < .001), more than three metastatic organs (p < .001), 11q23 loss of heterozygosity (LOH) (p = .007), and when more events occurred (p = .012). The 4-year EFS rate was significantly lower in patients with positive PHOX2B expression compared to the negative group at diagnosis (32.9% ± 6.2% vs. 74.5% ± 10.1%, p = .005). We stratified the 151 patients into three MRD risk groups: low high-risk (low-HR), with TP1 less than 10-4 and TP2 less than 10-4 ; ultra-HR, with TP1 greater than or equal to 10-2 or TP2 greater than or equal to 10-4 , and others classified as intermediate-HR. Patients in ultra-HR had the worst survival rate compared with other two groups (p = .02). In a multivariate model, MRD risk stratification based on PHOX2B levels at TP1 and TP2 was an independent prognostic factor for high-risk patients (p = .001). Patients in ultra-HR were associated with 11q23 LOH (p < .001), more than three organs of metastasis (p = .005), bone marrow metastasis (p < .001), and occurrence of more events (p = .009). CONCLUSIONS MRD risk stratification based on PHOX2B levels at two time points (after two and six cycles of induction chemotherapy) provided a stratification system for high-risk NB, which successfully predicted treatment outcomes. Our results present an effective method for further stratification of high-risk NB.
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Affiliation(s)
- Zhixia Yue
- Hematologic Disease Laboratory, Hematology Center, Beijing Key Laboratory of Pediatric Hematology Oncology, Beijing, China
- National Key Discipline of Pediatrics, Capital Medical University, Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
- Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Chao Gao
- Hematologic Disease Laboratory, Hematology Center, Beijing Key Laboratory of Pediatric Hematology Oncology, Beijing, China
- National Key Discipline of Pediatrics, Capital Medical University, Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
- Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Tianyu Xing
- Hematologic Disease Laboratory, Hematology Center, Beijing Key Laboratory of Pediatric Hematology Oncology, Beijing, China
- National Key Discipline of Pediatrics, Capital Medical University, Beijing, China
- Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
- Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Wen Zhao
- Medical Oncology Department, Pediatric Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology Oncology, Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
| | - Chao Duan
- Medical Oncology Department, Pediatric Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology Oncology, Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
| | - Xisi Wang
- Medical Oncology Department, Pediatric Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology Oncology, Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
| | - Mei Jin
- Medical Oncology Department, Pediatric Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology Oncology, Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
| | - Yan Su
- Medical Oncology Department, Pediatric Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
- Beijing Key Laboratory of Pediatric Hematology Oncology, Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing, China
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9
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Hutchins SC, Ferguson SR, Li G, Beierle EA, Alva E. BRAF mutation in neuroblastoma: A rare finding. Pediatr Blood Cancer 2023; 70:e29945. [PMID: 36069597 DOI: 10.1002/pbc.29945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/03/2022] [Accepted: 08/05/2022] [Indexed: 01/09/2023]
Affiliation(s)
- Sara C Hutchins
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Sara R Ferguson
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Geling Li
- Department of Pathology, Children's of Alabama, Birmingham, Alabama, USA
| | - Elizabeth A Beierle
- Division of Pediatric Surgery, Department of Surgery, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Elizabeth Alva
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
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van Zogchel LMJ, Lak NSM, Gelineau NU, Sergeeva I, Stelloo E, Swennenhuis J, Feitsma H, van Min M, Splinter E, Bleijs M, Groot Koerkamp M, Breunis W, Meister MT, Kholossy WH, Holstege FCP, Molenaar JJ, de Leng WWJ, Stutterheim J, van der Schoot CE, Tytgat GAM. Targeted locus amplification to develop robust patient-specific assays for liquid biopsies in pediatric solid tumors. Front Oncol 2023; 13:1124737. [PMID: 37152023 PMCID: PMC10157037 DOI: 10.3389/fonc.2023.1124737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/27/2023] [Indexed: 05/09/2023] Open
Abstract
Background Liquid biopsies combine minimally invasive sample collection with sensitive detection of residual disease. Pediatric malignancies harbor tumor-driving copy number alterations or fusion genes, rather than recurrent point mutations. These regions contain tumor-specific DNA breakpoint sequences. We investigated the feasibility to use these breakpoints to design patient-specific markers to detect tumor-derived cell-free DNA (cfDNA) in plasma from patients with pediatric solid tumors. Materials and methods Regions of interest (ROI) were identified through standard clinical diagnostic pipelines, using SNP array for CNAs, and FISH or RT-qPCR for fusion genes. Using targeted locus amplification (TLA) on tumor organoids grown from tumor material or targeted locus capture (TLC) on FFPE material, ROI-specific primers and probes were designed, which were used to design droplet digital PCR (ddPCR) assays. cfDNA from patient plasma at diagnosis and during therapy was analyzed. Results TLA was performed on material from 2 rhabdomyosarcoma, 1 Ewing sarcoma and 3 neuroblastoma. FFPE-TLC was performed on 8 neuroblastoma tumors. For all patients, at least one patient-specific ddPCR was successfully designed and in all diagnostic plasma samples the patient-specific markers were detected. In the rhabdomyosarcoma and Ewing sarcoma patients, all samples after start of therapy were negative. In neuroblastoma patients, presence of patient-specific markers in cfDNA tracked tumor burden, decreasing during induction therapy, disappearing at complete remission and re-appearing at relapse. Conclusion We demonstrate the feasibility to determine tumor-specific breakpoints using TLA/TLC in different pediatric solid tumors and use these for analysis of cfDNA from plasma. Considering the high prevalence of CNAs and fusion genes in pediatric solid tumors, this approach holds great promise and deserves further study in a larger cohort with standardized plasma sampling protocols.
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Affiliation(s)
- Lieke M. J. van Zogchel
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
- Sanquin Research and Landsteiner Laboratory of the AMC‐ University of Amsterdam, Department of Experimental Immunohematology, Amsterdam, Netherlands
| | - Nathalie S. M. Lak
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
- Sanquin Research and Landsteiner Laboratory of the AMC‐ University of Amsterdam, Department of Experimental Immunohematology, Amsterdam, Netherlands
| | - Nina U. Gelineau
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
- Sanquin Research and Landsteiner Laboratory of the AMC‐ University of Amsterdam, Department of Experimental Immunohematology, Amsterdam, Netherlands
| | | | | | | | | | | | | | - Margit Bleijs
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
| | | | - Willemijn Breunis
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
- University Children’s Hospital Zürich, Zürich, Switzerland
| | - Michael Torsten Meister
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | | | - Frank C. P. Holstege
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
- Center for Molecular Medicine, University Medical Center (UMC) Utrecht and Utrecht University, Utrecht, Netherlands
| | - Jan J. Molenaar
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
| | - Wendy W. J. de Leng
- Department of Pathology, University Medical Center (UMC) Utrecht, Utrecht, Netherlands
| | - Janine Stutterheim
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
| | - C. Ellen van der Schoot
- Sanquin Research and Landsteiner Laboratory of the AMC‐ University of Amsterdam, Department of Experimental Immunohematology, Amsterdam, Netherlands
| | - Godelieve A. M. Tytgat
- Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands
- *Correspondence: Godelieve A. M. Tytgat,
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Aktaş TÇ, Kızmazoğlu D, Aktaş S, Gökbayrak ÖE, Serinan E, Erol A, Altun Z, Yuan H, Olgun HN. Identification of ALK Mutation in Neuroblastoma on the Point of Molecular Heterogeneity. Technol Cancer Res Treat 2023; 22:15330338231211138. [PMID: 37964559 PMCID: PMC10652808 DOI: 10.1177/15330338231211138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 09/18/2023] [Accepted: 10/10/2023] [Indexed: 11/16/2023] Open
Abstract
BACKGROUND AND AIM In neuroblastoma, anaplastic lymphoma kinase mutations have recently received attention as molecular targets for the treatment of neuroblastoma, as 6% to 10% of patients with neuroblastoma have anaplastic lymphoma kinase mutations. There are little data from the cases in Turkey. We aimed to detect anaplastic lymphoma kinase mutations and molecular heterogeneity in neuroblastoma using next-generation sequencing. This study is the first one with this many cases in Turkey. METHODS Next-generation sequencing analysis was performed using an Illumina MiniSeq custom gene panel. Clinically important mutations were selected for the analysis. We also gathered clinical data of the patients from Turkish Pediatric Oncology Group cohorts to associate them with anaplastic lymphoma kinase mutations. This study is a retrospective cross-sectional study. We followed STROBE guideline (https://www.equator-network.org/reporting-guidelines/strobe/) on this study. RESULTS We analyzed anaplastic lymphoma kinase in 108 patients with neuroblastoma, with a mean age of 43.76 months. Pathogenic anaplastic lymphoma kinase mutations were detected in 13 patients (12.04%). We noted that anaplastic lymphoma kinase mutations were primarily observed in intermediate- and high-risk patients (P = .028). R1275Q and F1174-related mutations were predominant; I1171T, L1226F, S1189F, V1135A, and G1125S mutations were rare. Duplicate samples did not exhibit any heterogeneity. CONCLUSIONS We found that F1174 and R1275Q-related anaplastic lymphoma kinase mutations are the most common pathogenic mutations in neuroblastoma. Anaplastic lymphoma kinase mutation status did not show any heterogeneity, and the mutations were correlated with intermediate- or high-risk groups.
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Affiliation(s)
- Tekincan Çağrı Aktaş
- Institute of Oncology, Department of Basic Oncology, Dokuz Eylül University, Izmir, Turkey
| | - Deniz Kızmazoğlu
- Institute of Oncology, Department of Clinical Oncology, Dokuz Eylül University, Izmir, Turkey
| | - Safiye Aktaş
- Institute of Oncology, Department of Basic Oncology, Dokuz Eylül University, Izmir, Turkey
| | - Özde Elif Gökbayrak
- Institute of Oncology, Department of Basic Oncology, Dokuz Eylül University, Izmir, Turkey
| | - Efe Serinan
- Institute of Oncology, Department of Basic Oncology, Dokuz Eylül University, Izmir, Turkey
| | - Aylin Erol
- Institute of Oncology, Department of Basic Oncology, Dokuz Eylül University, Izmir, Turkey
| | - Zekiye Altun
- Institute of Oncology, Department of Basic Oncology, Dokuz Eylül University, Izmir, Turkey
| | - Hongling Yuan
- Institute of Oncology, Department of Basic Oncology, Dokuz Eylül University, Izmir, Turkey
| | - Hatice Nur Olgun
- Institute of Oncology, Department of Clinical Oncology, Dokuz Eylül University, Izmir, Turkey
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Pancancer Analyses Reveal Genomics and Clinical Characteristics of the SETDB1 in Human Tumors. JOURNAL OF ONCOLOGY 2022; 2022:6115878. [PMID: 35656340 PMCID: PMC9152430 DOI: 10.1155/2022/6115878] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/17/2022] [Indexed: 12/03/2022]
Abstract
Background. Malignant tumor is one of the most common diseases that seriously affect human health. The prior literature has reported the biological function and potential therapeutic targets of SET domain bifurcated histone lysine methyltransferase 1 (SETDB1) as an oncogene. However, SETDB1 has rarely been analyzed from a pan-cancer perspective. Methods. Bioinformatics analysis tools and databases, including GeneCards, National Center for Biotechnology Information (NCBI), UniProt, Illustrator for Biological Sequences (IBS), Human Protein Atlas (HPA), GEPIA, TIMER2, Sangerbox 3.0, UALCAN, Kaplan-Meier (K-M) plotter, cBioPortal, Catalogue Of Somatic Mutations In Cancer (COSMIC), PhosphoSitePlus, TISIDB, STRING, and GeneMANIA, were utilized to clarify the biological functions and clinical significance of SETDB1 from a pan-cancer perspective. Results. In this study, the pan-cancer analysis demonstrated that SETDB1 showed significantly differential expression in most tumor tissues and paracancerous tissues, and SETDB1 expression was associated with clinicopathological features and clinical prognosis. We also found that SETDB1 mutations occurred in most tumors and were related to tumorigenesis. In addition, DNA methylation of SETDB1 primarily occurred at the cg10444928 site and was associated with prognosis in several human tumors. The predicted phosphorylation site of SETDB1 was Ser1006. We found that SETDB1 was significantly related to the specific tumor-infiltrating immune cell populations and expression of clinically targetable immune checkpoints and may be a promising immunotherapy target. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses also indicated that SETDB1 may function as crucial regulator in carcinogenesis of human cancers. Conclusions. SETDB1 is an important oncogene involved in tumorigenesis and tumor progression through different biological mechanisms. Furthermore, SETDB1 may be a potential therapeutic target for cancer treatment.
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Lu XY, Qu LJ, Duan XL, Zuo W, Sai K, Rui G, Gong XF, Ding YB, Gao Q. Impact of 11q Loss of Heterozygosity Status on the Response of High-Risk Neuroblastoma With MYCN Amplification to Neoadjuvant Chemotherapy. Front Pediatr 2022; 10:898918. [PMID: 35757140 PMCID: PMC9226623 DOI: 10.3389/fped.2022.898918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 05/06/2022] [Indexed: 11/16/2022] Open
Abstract
PURPOSE The aim of this study was to investigate whether 11q loss of heterozygosity (LOH) aberration would impact the response of the primary tumor to neoadjuvant chemotherapy or to the degree of surgical resection in neuroblastoma (NB) patients with MYCN amplification. METHODS The clinical data of 42 NB patients with MYCN amplification who were newly diagnosed and received treatments at our hospital from 2011 to 2020 were retrospectively analyzed. According to the results of the segmental chromosome aberration analysis, the patients enrolled were assigned to an 11qLOH positive group and an 11qLOH negative group. RESULTS There was no significant difference in the mean number of chemotherapy courses completed before surgery between the 11qLOH positive and 11qLOH negative groups (p = 0.242). Each of the 42 patients had metaiodobenzylguanidine (MIBG) scans both before and after neoadjuvant chemotherapy. The percentage of patients who had a clinical MIBG change in the 11qLOH positive group was lower than the percentage in the 11qLOH negative group (27.27 vs. 66.67%, p = 0.030). The 11qLOH negative group seemed to have a higher rate of surgical resection (≥90%); however, the difference between the two groups was not statistically significant (p = 0.088). Furthermore, the 11qLOH negative group did not show significantly superior event-free survival and overall survival rates compared with the 11qLOH positive group. CONCLUSIONS This study showed that patients with NB and MYCN amplification in combination with 11qLOH might be less likely to respond to neoadjuvant chemotherapy when compared with patients with NB and MYCN amplification without 11qLOH.
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Affiliation(s)
- Xian-Ying Lu
- Department of General Surgery, Anhui Children's Hospital, Hefei, China
| | - Li-Jun Qu
- Department of Hematology and Oncology, Anhui Children's Hospital, Hefei, China
| | - Xian-Lun Duan
- Department of Thoracic Surgery, Anhui Children's Hospital, Hefei, China
| | - Wei Zuo
- Department of Neonatal Surgery, Anhui Children's Hospital, Hefei, China
| | - Kai Sai
- Department of General Surgery, Anhui Children's Hospital, Hefei, China
| | - Gang Rui
- Department of General Surgery, Anhui Children's Hospital, Hefei, China
| | - Xian-Feng Gong
- Department of General Surgery, Anhui Children's Hospital, Hefei, China
| | - Yi-Bo Ding
- Department of General Surgery, Anhui Children's Hospital, Hefei, China
| | - Qun Gao
- Department of General Surgery, Anhui Children's Hospital, Hefei, China
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